README.md

In ngsReports: Load FastqQC reports and other NGS related files

ngsReports

An R Package for managing FastQC reports and other NGS related log files inside R. Except for some periodic minor bug fixes, this branch is the current release which is also available from the Bioconductor website. To install this package for Bioconductor <= 3.6 (R <= 3.4.4) please use the drop down menu above to change to the branch Bioc3.6, and follow the instructions there. Versions for Bioc releases 3.9 and 3.10 are also available as branches from this repository.

Installation

To install required packages follow the instructions below.

install.packages("BiocManager")
BiocManager::install("steveped/ngsReports")
library(ngsReports)

Usage

The paper for the package can be found here. For a detailed usage guide please see here.

ShinyApp

A Graphical User Interface (Shiny App) has been developed for interactive inspection of many FastQC reports. The ngsReports shiny app can be installed here.

Tools Supported (By Category)

Quality control

• FastQC

Adapter removal and trimming

• AdapterRemoval
• CutAdapt
• Trimmomatic

Mapping and alignment

• Bowtie
• Bowtie2
• HISAT2
• Samtools flagstat
• STAR
• Picard MarkDuplicates

Transcript/gene quantificaiton

• Feature counts

Genome assembly

• BUSCO
• Quast

Citation

Please cite our paper:

@article{ward2018ngsreports,
    author = {Ward, Christopher M and To, Thu-Hien and Pederson, Stephen M},
    title = "{ngsReports: a Bioconductor package for managing FastQC reports and other NGS related log files}",
    journal = {Bioinformatics},
    year = {2019},
    month = {12},
    doi = {10.1093/bioinformatics/btz937},
    url = {https://doi.org/10.1093/bioinformatics/btz937}
}

ngsReports documentation built on Nov. 23, 2020, 2:01 a.m.